DNA motifs determining the accuracy of repeat duplication during CRISPR adaptation in Haloarcula hispanica

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) acquire new spacers to generate adaptive immunity in prokaryotes. During spacer integration, the leader-preceded repeat is always accurately duplicated, leading to speculations of a repeat-length ruler. Here in Haloarcula hispanica,...

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Bibliographic Details
Published in:Nucleic acids research 2016-05, Vol.44 (9), p.4266-4277
Main Authors: Wang, Rui, Li, Ming, Gong, Luyao, Hu, Songnian, Xiang, Hua
Format: Article
Language:English
Subjects:
Base Sequence
Clustered Regularly Interspaced Short Palindromic Repeats
DNA Replication
DNA, Archaeal - genetics
Gene Duplication
Genes, Archaeal
Haloarcula - genetics
Haloarcula hispanica
Molecular Biology
Nucleotide Motifs
Sequence Analysis, DNA
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Summary:Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) acquire new spacers to generate adaptive immunity in prokaryotes. During spacer integration, the leader-preceded repeat is always accurately duplicated, leading to speculations of a repeat-length ruler. Here in Haloarcula hispanica, we demonstrate that the accurate duplication of its 30-bp repeat requires two conserved mid-repeat motifs, AACCC and GTGGG. The AACCC motif was essential and needed to be ∼10 bp downstream from the leader-repeat junction site, where duplication consistently started. Interestingly, repeat duplication terminated sequence-independently and usually with a specific distance from the GTGGG motif, which seemingly served as an anchor site for a molecular ruler. Accordingly, altering the spacing between the two motifs led to an aberrant duplication size (29, 31, 32 or 33 bp). We propose the adaptation complex may recognize these mid-repeat elements to enable measuring the repeat DNA for spacer integration.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkw260